ontoportal · syphax-bouazzouni · Sep 23, 2022 · Dec 17, 2022 · Dec 17, 2022 · Dec 17, 2022
diff --git a/.gitignore b/.gitignore
@@ -25,7 +25,6 @@ migration/test*
 *.sublime-workspace
 
 # Rbenv artifacts
-.ruby-version
 test/test_run.log
 
 # Debug output

diff --git a/.ruby-version b/.ruby-version
@@ -0,0 +1 @@
+3.1.6
diff --git a/Dockerfile b/Dockerfile
@@ -1,22 +1,36 @@
-ARG RUBY_VERSION
-ARG DISTRO_NAME=bullseye
+ARG RUBY_VERSION=3.1
+ARG DISTRO=bullseye
 
-FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+FROM ruby:$RUBY_VERSION-$DISTRO
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-  openjdk-11-jre-headless \
-  raptor2-utils \
-  && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    git \
+    libxml2 \
+    libxslt-dev \
+    openjdk-11-jre-headless \
+    raptor2-utils \
+    && rm -rf /var/lib/apt/lists/*
 
-RUN mkdir -p /srv/ontoportal/ontologies_linked_data
-RUN mkdir -p /srv/ontoportal/bundle
-COPY Gemfile* /srv/ontoportal/ontologies_linked_data/
+WORKDIR /app
 
-WORKDIR /srv/ontoportal/ontologies_linked_data
+COPY Gemfile* *.gemspec ./
 
-RUN gem update --system
-RUN gem install bundler
-ENV BUNDLE_PATH=/srv/ontoportal/bundle
-RUN bundle install
+# Copy only the `version.rb` file to prevent missing file errors!
+COPY lib/ontologies_linked_data/version.rb lib/ontologies_linked_data/
 
-COPY . /srv/ontoportal/ontologies_linked_data
+#Install the exact Bundler version from Gemfile.lock (if it exists)
+RUN gem update --system && \
+    if [ -f Gemfile.lock ]; then \
+      BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \
+      gem install bundler -v "$BUNDLER_VERSION"; \
+    else \
+      gem install bundler; \
+    fi
+
+RUN bundle config set --global no-document 'true'
+RUN bundle install --jobs 4 --retry 3
+
+COPY . ./
+
+CMD ["bundle", "exec", "rake"]
diff --git a/Gemfile b/Gemfile
@@ -1,5 +1,7 @@
 source 'https://rubygems.org'
 
+gemspec
+
 gem 'activesupport', '~> 4'
 gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
@@ -37,6 +39,5 @@ end
 gem 'goo', github: 'ncbo/goo', branch: 'master'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
 
-gem 'net-ftp'
 gem 'public_suffix', '~> 5.1.1'
-gem 'net-imap', '~> 0.4.18'
+gem 'net-imap', '~> 0.4.18'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 39f67ab7fae7675b6ff417ace0ab923e40ffcbcd
+  revision: b9019ad9e1eb78c74105fc6c6a879085066da17d
   branch: master
   specs:
     goo (0.0.2)
@@ -24,6 +24,25 @@ GIT
       net-http-persistent (= 2.9.4)
       rdf (>= 1.0)
 
+PATH
+  remote: .
+  specs:
+    ontologies_linked_data (0.0.1)
+      activesupport
+      bcrypt
+      goo
+      json
+      libxml-ruby
+      multi_json
+      net-ftp
+      oj
+      omni_logger
+      pony
+      rack
+      rack-test
+      rsolr
+      rubyzip
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -36,15 +55,15 @@ GEM
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
-    ast (2.4.2)
+    ast (2.4.3)
     bcrypt (3.1.20)
     bigdecimal (3.1.9)
     builder (3.3.0)
     childprocess (5.1.0)
       logger (~> 1.5)
     coderay (1.1.3)
     concurrent-ruby (1.3.5)
-    connection_pool (2.5.0)
+    connection_pool (2.5.3)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     date (3.4.1)
@@ -55,31 +74,32 @@ GEM
       launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (2.12.2)
+    faraday (2.13.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
     faraday-net_http (3.4.0)
       net-http (>= 0.5.0)
-    ffi (1.17.1-aarch64-linux-gnu)
-    ffi (1.17.1-arm64-darwin)
-    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.2-aarch64-linux-gnu)
+    ffi (1.17.2-arm64-darwin)
+    ffi (1.17.2-x86_64-linux-gnu)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.8)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.10.1)
+    json (2.11.3)
     json_pure (2.8.1)
     language_server-protocol (3.17.0.4)
-    launchy (3.1.0)
+    launchy (3.1.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
       logger (~> 1.6)
     libxml-ruby (5.0.3)
-    logger (1.6.5)
+    lint_roller (1.1.0)
+    logger (1.7.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -88,10 +108,10 @@ GEM
       net-pop
       net-smtp
     method_source (1.1.0)
-    mime-types (3.6.0)
+    mime-types (3.6.2)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0204)
+    mime-types-data (3.2025.0422)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -106,7 +126,7 @@ GEM
     net-http (0.6.0)
       uri
     net-http-persistent (2.9.4)
-    net-imap (0.4.19)
+    net-imap (0.4.21)
       date
       net-protocol
     net-pop (0.1.2)
@@ -116,35 +136,36 @@ GEM
     net-smtp (0.5.1)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.9)
+    oj (3.16.10)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     ostruct (0.6.1)
-    parallel (1.26.3)
-    parser (3.3.7.1)
+    parallel (1.27.0)
+    parser (3.3.8.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
       mail (>= 2.0)
     powerbar (2.0.1)
       hashie (>= 1.1.0)
+    prism (1.4.0)
     pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
     racc (1.8.1)
-    rack (2.2.11)
+    rack (2.2.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rainbow (3.1.1)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.3.0)
+    redis (5.4.0)
       redis-client (>= 0.22.0)
-    redis-client (0.23.2)
+    redis-client (0.24.0)
       connection_pool
     regexp_parser (2.10.0)
     request_store (1.7.0)
@@ -154,22 +175,24 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.4.0)
+    rexml (3.4.1)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.71.2)
+    rubocop (1.75.4)
       json (~> 2.3)
-      language_server-protocol (>= 3.17.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.9.3, < 3.0)
-      rubocop-ast (>= 1.38.0, < 2.0)
+      rubocop-ast (>= 1.44.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.38.0)
-      parser (>= 3.3.1.0)
+    rubocop-ast (1.44.1)
+      parser (>= 3.3.7.2)
+      prism (~> 1.4)
     ruby-progressbar (1.13.0)
     rubyzip (1.3.0)
     simplecov (0.22.0)
@@ -194,15 +217,14 @@ GEM
     unicode-display_width (3.1.4)
       unicode-emoji (~> 4.0, >= 4.0.4)
     unicode-emoji (4.0.4)
-    uri (1.0.2)
+    uri (1.0.3)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
   arm64-darwin-23
-  arm64-darwin-24
   x86_64-linux
 
 DEPENDENCIES
@@ -217,10 +239,10 @@ DEPENDENCIES
   minitest (~> 4)
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
-  net-ftp
   net-imap (~> 0.4.18)
   oj (~> 3.0)
   omni_logger
+  ontologies_linked_data!
   pony
   pry
   public_suffix (~> 5.1.1)
@@ -238,4 +260,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.4.22
+   2.6.3
diff --git a/bin/owlapi-wrapper-1.4.2.jar b/bin/owlapi-wrapper-1.4.2.jar
diff --git a/bin/owlapi-wrapper-1.4.3.jar b/bin/owlapi-wrapper-1.4.3.jar